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geneontology / pipeline

Declarative pipeline for the Gene Ontology.
https://build.geneontology.org/job/geneontology/job/pipeline/
BSD 3-Clause "New" or "Revised" License
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Switch EBI URLs in the metadata from ftp to http(s) schema #304

Closed kltm closed 1 year ago

kltm commented 1 year ago

To improve reliability and usability in the pipeline, we'd like to switch away from FTP. Can't hurt and FTP unlikely to be around forever.

kltm commented 1 year ago

I seem to recall that some file was unavailable w/a non-ftp schema, but a sampling says that either I'm misremembering or that has changed.

kltm commented 1 year ago

Okay, I think I'm conflating this with the state of the mapping files from a while ago.

kltm commented 1 year ago

@balhoff @pgaudet Since between noon and 6pm PT time on the 25th, the go-ontology-dev pipeline has been unable to complete, hanging essentially indefinitely on downloading chebi. I'm wondering if they are throttling us? Would you know of any contacts to follow up on? Otherwise, we'll need to switch back to FTP--it didn't always work, but it could complete.

kltm commented 1 year ago

Have temporarily suspended go-ontology-dev

kltm commented 1 year ago

Also see: https://github.com/geneontology/pipeline/issues/305

kltm commented 1 year ago

We've hit a new problem with slowdowns, but this metadata update is done.